Cruise departing/arriving in Rome. Have 2 days to spend in Italy before Cruise, where to go?

Florence for the art or Venice for the atmosphere. Each will easily keep you busy for two days. If you want, Siena can be done as a daytrip from Florence (by bus or train), and Padua, Vicenza or Verona from Venice (very frequent train connections). Chances are you will enjoy Venice more.
If I understand your schedule correctly, it would be best to fly into Florence or Venice and then pick up your cruise in Rome, and do Rome after the cruise before flying back home.
Both are connected to Rome (Termini station) by hourly direct, fast trains. Florence is 1,5 hrs away and Venice a little bit under 4 hrs.

If my understanding is correct (and it may not be), you will have 3 full days before the cruise and some amount of time after the cruise ends in Rome. If that is the case, consider flying in to Venice, spending two days there, using the third day to get to Rome, and then spending time in Rome at the end of the cruise. On the other hand, one can easily spend a full week in Rome and still not see or do it all so you might want to use all your time there. It seems that it always takes more time to go from one location to another than anticipated, and that is time you can't recover.

First, I would spend the whole two days in Rome. Why run to somewhere else? When we do cruises we tend to come a week early and stay a week later. Gives us time to do other things but if you are only arriving three days early then there is little point in going somewhere else. Your first day anywhere is going to be lost via jet lag. Then two (?) full days to do something and then a fourth day is getting to the port. If going to Venice, or Florence, anywhere you are going to spend a big chunk of time looking out railroad windows. Do you really want to do that?

What are your return plans? Going home the day you dock? Remember the port for Rome is over an hour from Rome via train you need to take that into consideration. And a couple hours via train to the airport. How about planning a week after the cruises ends. Then you could travel to Florence or Venice or Milan and come home from Milan or Venice. You need to think about some alternatives around the cruise.

Fly into Venice and spend 2 or 3 (??) nights before getting the high speed train (3hr 45min) to Rome.

If you post which ports your cruise is stopping in, people can give better advice.